--------------------------------------------- # Raw birdsong data for "Vocal changes in a zebra finch model of Parkinson’s Disease characterized by alpha-synuclein overexpression in the song-dedicated anterior forebrain pathway" Preferred Citation: Medina, Cesar A.; Vargas, Eddie; Munger, Stephanie; Miller, Julie Elizabeth (2022): Raw birdsong data for "Vocal changes in a zebra finch model of Parkinson’s Disease characterized by alpha-synuclein overexpression in the song-dedicated anterior forebrain pathway". University of Arizona Research Data Repository. Dataset. https://doi.org/10.25422/azu.data.16619782 Corresponding Author: Julie E. Miller, University of Arizona, juliemiller@arizona.edu License: CC BY 4.0 DOI: https://doi.org/10.25422/azu.data.16619782 --------------------------------------------- ## Summary Parkinson's disease is the second most common neurodegenerative disease affecting motor behavior. In addition to the typical peripheral limb motor symptoms, vocal motor issues such as deteriorated vocal quality are present in Parkinson's patients. Unfortunately, very little is known about the biological mechanisms underlying these vocal changes. Here, we developed a Parkinsonian model using the zebra finch songbird to study the underlying neural mechanisms of these changes. Finch song and supportive brain areas are similar to human speech and brain pathways. To do this, we recorded song for 2 hours from zebra finches injected with an adeno-associated virus expressing either the causally-related human Parkinsonian gene SNCA or control GFP protein in finch brain. Song was then segmented using a specially designed matlab program called Vocal Inventory Clustering Engine (VoICE) into unique syllables. Acoustic features such as duration, pitch, mean frequency, amplitude, Wiener Entropy, frequency modulation, and amplitude modulation were measured from 75 individual copies of these syllables. The mean, mean variance, and coefficient of variation of these syllables were also measured. Motif-level data was also collected to monitor how much each bird sang (i.e., how many copies of song were uttered over a 2 hour period). We found that overexpression of SNCA led to shorter and poorer quality syllables that are similar to Parkinsonian vocal changes. To cite this work, please cite both the associated PLoS One paper "Vocal changes in a zebra finch model of Parkinson’s Disease characterized by alpha-synuclein overexpression in the song-dedicated anterior forebrain pathway" (https://doi.org/10.1371/journal.pone.0265604) and this dataset. The data are audio .wav files of birdsong from alpha-synuclein overexpressing, GFP control, and non-surgical adult male zebra finches. These .wav files were analyzed in the above mentioned citation. Briefly, the "SyllableData" directory contains cut .wav file of a single syllable rendition - syllables being the most basic unit of song - from the birds used in the above mentioned citation. The "MotifData" directory contains two hours of .wav files for each day of recording - a motif being a basic unit of birdsong - from the birds used in the above mentioned citation. The audio files can be played in Windows Media Player or opened in freeware (e.g., Audacity, Praat) to view as a wave form or spectrogram. --------------------------------------------- ## Files and Folders ### Naming convention: Individual audio folders are named based on leg band color: Bk-Black, Wh-White, Rd-Red and the number of the bird. This makes up the subjects BirdID. The audio files are included in .zip files corresponding to syllable and motif level data. #### Syllable Data Folders in the "SyllableData" folder follow this architecture: BirdID | BirdID_[Insert Date] | BirdID_[Insert Date]_WAV_[Syllable Name] | .wav files The date corresponds to when the syllable was recorded. Syllable Name serves as syllable unique identifier. Around 25 renditions per syllable exist. #### Motif Data Folders in the "MotifData" folder follow this architecture: BirdID | BirdID_[Timepoint]_[Day] | .wav files The Timepoints: Post1, Post2, Post3, and Pre, correspond to timepoints 1, 2, 3, and 0 month respectively. The day from 1-3 correspond to date of recording. Around 3 days of song per timepoint were recorded. ### Master List Master list contains four columns. BirdID corresponds to animal unique subject number. SyllableData indicates whether syllable-level data was extracted from this animal with either a "Yes" or "No". MotifData indicates whether motif-level data was extracted from this animal with either a "Yes" or "No". Condition indicates the animal's experimental condition with either "asyn" for alpha-synuclein overexpressing group, "gfp" for GFP expressing group, or "non" for non-surgical group. BirdID SyllableData MotifData Condition Bk174 Yes No asyn Bk262 Yes Yes asyn Bk268 Yes Yes gfp Bk277 Yes Yes gfp Bk278 Yes Yes asyn Bk280 Yes Yes asyn Bk286 Yes Yes gfp Bk293 Yes Yes asyn Bk295 Yes Yes asyn Rd321 Yes No asyn Rd346 No Yes gfp Wh145 Yes No gfp Wh203 Yes Yes asyn Wh206 Yes Yes asyn Wh211 Yes Yes gfp Wh214 Yes No asyn Wh412 No Yes gfp Wh422 No Yes asyn Wh423 No Yes gfp Wh436 No Yes asyn Wh470 No Yes gfp Wh840 No Yes non Wh845 No Yes non Wh848 No Yes non Wh853 No Yes non ### Syllable Type Syllable type contains 2 columns. Bird.Syll corresponds to syllable from animal subject. Syllable.Type indicates type of syllable based on Badwal et al. published during 2020 in the Behavioral Neuroscience journal (citation below). Badwal, A., Borgstrom, M., Samlan, R. A., & Miller, J. E. (2020, March 12). "Middle Age, a Key Time Point for Changes in Birdsong and Human Voice." Behavioral Neuroscience. 134(3):208-221. doi: 10.1037/bne0000363 Epub Mar 12. Bird.Syll Syllable.Type Bk174.D Harmonic Bk262.C Harmonic Bk262.E Harmonic Bk268.E Harmonic Bk268.F Harmonic Bk277.A Harmonic Bk277.B Harmonic Bk277.F Harmonic Bk278.C Harmonic Bk278.E Harmonic Bk278.F Harmonic Bk280.D Harmonic Bk293.B Harmonic Bk293.E Harmonic Bk295.C Harmonic Bk295.F Harmonic Rd321.D Harmonic Rd346.B Harmonic Rd346.E Harmonic Wh145.B Harmonic Wh145.D Harmonic Wh203.B Harmonic Wh203.F Harmonic Wh206.D Harmonic Wh211.E Harmonic Wh211.F Harmonic Wh214.F Harmonic Wh214.G Harmonic Bk174.C Mixed Bk174.E Mixed Bk262.B Mixed Bk262.D Mixed Bk268.D Mixed Bk277.E Mixed Bk277.G Mixed Bk278.B Mixed Bk280.A Mixed Bk280.B Mixed Bk286.C Mixed Bk293.D Mixed Bk293.F Mixed Bk295.B Mixed Bk295.E Mixed Rd321.C Mixed Rd321.E Mixed Rd346.A Mixed Rd346.D Mixed Rd346.F Mixed Wh145.C Mixed Wh145.E Mixed Wh203.C Mixed Wh203.D Mixed Wh206.C Mixed Wh206.E Mixed Wh206.F Mixed Wh211.B Mixed Wh211.G Mixed Wh214.E Mixed Bk174.B Noisy Bk268.C Noisy Bk277.D Noisy Bk280.C Noisy Bk286.A Noisy Bk286.B Noisy Bk295.D Noisy Rd321.B Noisy Wh145.A Noisy Wh203.G Noisy Wh203.H Noisy Wh206.B Noisy Wh211.C Noisy Wh211.D Noisy Wh214.C Noisy Wh214.D Noisy Bk174.A Slide Bk262.A Slide Bk268.A Slide Bk268.B Slide Bk277.C Slide Bk278.A Slide Bk278.D Slide Bk293.A Slide Bk293.C Slide Bk295.A Slide Rd321.A Slide Rd346.C Slide Wh203.A Slide Wh203.E Slide Wh206.A Slide Wh211.A Slide Wh214.A Slide Wh214.B Slide SyllableTypes.pptx file contains images of syllable types determined by authors. Categories include Mixed, Slide, Noisy, and Harmonic. Within Harmonic exists a special class called FlatHarmonic that were also analyzed independently. ### Experimental Time Window list Experimental time window list contains five columns. BirdID corresponds to animal unique subject number. Timepoint corresponds to timepoint, where 0 is pre and 1-3 are post-timepoints. Day corresponds to day with at least 3 days of song collected per time point. Wav.Beginning if not "NA" indicates the name of the file when the 2-hour song-session was determined to begin and if an "NA" then that means that data does not exist. Wav.End if not "NA" indicates the name of the file when the 2-hour song-session was determined to end and if an "NA" then that means that data does not exist. BirdID Timepoint Day Wav.Beginning Wav.End Bk174 0 1 NA NA Bk174 0 2 NA NA Bk174 0 3 NA NA Bk174 1 1 NA NA Bk174 1 2 NA NA Bk174 1 3 NA NA Bk174 2 1 NA NA Bk174 2 2 NA NA Bk174 2 3 NA NA Bk174 3 1 NA NA Bk174 3 2 NA NA Bk174 3 3 NA NA Bk262 0 1 Bk262_May_19_2016_27153607 Bk262_May_19_2016_34350813 Bk262 0 2 Bk262_May_20_2016_29378075 Bk262_May_20_2016_36597751 Bk262 0 3 Bk262_May_22_2016_27212861 Bk262_May_22_2016_34391442 Bk262 1 1 Bk262_July_02_2016_27193525 Bk262_July_02_2016_34345464 Bk262 1 2 Bk262_July_03_2016_27189349 Bk262_July_03_2016_34404665 Bk262 1 3 Bk262_July_04_2016_27183803 Bk262_July_04_2016_34379337 Bk262 2 1 Bk262_August_04_2016_27183097 Bk262_August_04_2016_34374263 Bk262 2 2 Bk262_August_05_2016_27272575 Bk262_August_05_2016_34471612 Bk262 2 3 Bk262_August_06_2016_27217814 Bk262_August_06_2016_34412509 Bk262 3 1 Bk262_September_03_2016_27323543 Bk262_September_03_2016_34516236 Bk262 3 2 Bk262_September_04_2016_27407709 Bk262_September_04_2016_33219698 Bk262 3 3 Bk262_September_05_2016_27636849 Bk262_September_05_2016_34736054 Bk268 0 1 Bk268a_May_22_2016_27129470 Bk268a_May_22_2016_34248537 Bk268 0 2 Bk268a_May_23_2016_27111418 Bk268a_May_23_2016_33639148 Bk268 0 3 Bk268a_June_01_2016_27051823 Bk268a_June_01_2016_34236853 Bk268 1 1 Bk268_July_02_2016_27125207 Bk268_July_02_2016_33767422 Bk268 1 2 Bk268_July_03_2016_27044357 Bk268_July_03_2016_34246330 Bk268 1 3 Bk268_July_04_2016_27071965 Bk268_July_04_2016_34081193 Bk268 2 1 Bk268_August_04_2016_26918740 Bk268_August_04_2016_34073501 Bk268 2 2 Bk268_August_05_2016_26938772 Bk268_August_05_2016_34093721 Bk268 2 3 Bk268_August_06_2016_26946822 Bk268_August_06_2016_33775261 Bk268 3 1 NA NA Bk268 3 2 Bk268_September_04_2016_27044052 Bk268_September_04_2016_34228646 Bk268 3 3 Bk268_September_05_2016_26949447 Bk268_September_05_2016_34143365 Bk277 0 1 Bk277_May_26_2016_27539962 Bk277_May_26_2016_34728943 Bk277 0 2 Bk277_May_28_2016_27189536 Bk277_May_28_2016_34373129 Bk277 0 3 Bk277_May_29_2016_27528958 Bk277_May_29_2016_34721351 Bk277 1 1 Bk277_June_27_2016_27112643 Bk277_June_27_2016_34087731 Bk277 1 2 Bk277_June_28_2016_28023279 Bk277_June_28_2016_35097846 Bk277 1 3 Bk277_July_01_2016_27336867 Bk277_July_01_2016_34509066 Bk277 2 1 Bk277_July_30_2016_27128148 Bk277_July_30_2016_34308541 Bk277 2 2 Bk277_July_31_2016_27112582 Bk277_July_31_2016_34311008 Bk277 2 3 Bk277_August_03_2016_27349394 Bk277_August_03_2016_34544052 Bk277 3 1 Bk277_August_28_2016_27077631 Bk277_August_28_2016_34288779 Bk277 3 2 Bk277_August_29_2016_27095659 Bk277_August_29_2016_34261118 Bk277 3 3 Bk277_September_01_2016_27492566 Bk277_September_01_2016_34126642 Bk278 0 1 Bk278_May_21_2016_28091128 Bk278_May_21_2016_35281226 Bk278 0 2 Bk278_May_22_2016_27615873 Bk278_May_22_2016_34816398 Bk278 0 3 Bk278_May_23_2016_27441600 Bk278_May_23_2016_34604171 Bk278 1 1 Bk278_July_02_2016_27465587 Bk278_July_02_2016_34688883 Bk278 1 2 Bk278_July_03_2016_27727079 Bk278_July_03_2016_34720953 Bk278 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Wh423_December_06_2017_34752552 Wh423 1 4 Wh423_December_07_2017_27276836 Wh423_December_07_2017_34470579 Wh423 1 5 Wh423_December_08_2017_27304986 Wh423_December_08_2017_34491894 Wh436 0 1 Wh436_November_12_2017_27465183 Wh436_November_12_2017_34680641 Wh436 0 2 Wh436_November_13_2017_27691568 Wh436_November_13_2017_34874169 Wh436 0 3 Wh436_November_14_2017_27468327 Wh436_November_14_2017_34664033 Wh436 1 1 Wh436_December_23_2017_27382327 Wh436_December_23_2017_34521965 Wh436 1 2 Wh436_December_24_2017_27301164 Wh436_December_24_2017_34477761 Wh436 1 3 Wh436_December_25_2017_27244898 Wh436_December_25_2017_34394122 Wh436 2 1 Wh436_January_17_2018_30668662 Wh436_January_17_2018_37853368 Wh436 2 2 Wh436_January_18_2018_27420895 Wh436_January_18_2018_33375019 Wh436 2 3 Wh436_January_20_2018_27272865 Wh436_January_20_2018_34187047 Wh470 0 1 Wh470_November_08_2017_28970484 Wh470_November_08_2017_36135020 Wh470 0 2 Wh470_November_09_2017_27234031 Wh470_November_09_2017_34441205 Wh470 0 3 Wh470_November_10_2017_27131121 Wh470_November_10_2017_34298990 Wh470 0 4 Wh470_November_11_2017_27322674 Wh470_November_11_2017_30655408 Wh470 1 1 NA NA Wh470 1 2 Wh470_December_17_2017_27011721 Wh470_December_17_2017_34203638 Wh470 1 3 Wh470_December_18_2017_27230570 Wh470_December_18_2017_34393145 Wh470 2 1 Wh470_January_09_2018_29257759 Wh470_January_09_2018_35183523 Wh470 2 2 Wh470_January_10_2018_27072070 Wh470_January_10_2018_34262812 Wh470 2 3 Wh470_January_11_2018_27219568 Wh470_January_11_2018_34420666 Wh470 3 1 Wh470_February_09_2018_32429993 Wh470_February_09_2018_38502140 Wh470 3 2 Wh470_February_10_2018_26981424 Wh470_February_10_2018_34165379 Wh470 3 3 Wh470_February_11_2018_27013292 Wh470_February_11_2018_34097033 Wh470 3 4 Wh470_February_12_2018_27031252 Wh470_February_12_2018_34228415 Wh840 0 1 Wh840_July_02_2020_28300221 Wh840_July_02_2020_35477610 Wh840 0 2 Wh840_July_03_2020_27060553 Wh840_July_03_2020_34225694 Wh840 0 3 Wh840_July_04_2020_26926793 Wh840_July_04_2020_34116715 Wh840 0 4 Wh840_July_05_2020_26934674 Wh840_July_05_2020_34139984 Wh840 0 5 Wh840_July_06_2020_26954970 Wh840_July_06_2020_34152273 Wh840 0 6 Wh840_July_07_2020_28203088 Wh840_July_07_2020_35329470 Wh845 0 1 Wh845_July_04_2020_31781769 Wh845_July_04_2020_38968630 Wh845 0 2 Wh845_July_05_2020_29416291 Wh845_July_05_2020_35774144 Wh845 0 3 Wh845_July_06_2020_28154284 Wh845_July_06_2020_35344374 Wh845 0 4 Wh845_July_07_2020_28016628 Wh845_July_07_2020_34392321 Wh845 0 5 Wh845_July_08_2020_28552274 Wh845_July_08_2020_35619535 Wh848 0 1 Wh848_July_02_2020_27093969 Wh848_July_02_2020_32225342 Wh848 0 2 Wh848_July_03_2020_26996598 Wh848_July_03_2020_34198300 Wh848 0 3 Wh848_July_04_2020_26970362 Wh848_July_04_2020_33628044 Wh848 0 4 Wh848_July_05_2020_26965539 Wh848_July_05_2020_34185349 Wh848 0 5 Wh848_July_06_2020_26980844 Wh848_July_06_2020_34160406 Wh848 0 6 Wh848_July_07_2020_28023286 Wh848_July_07_2020_35040959 Wh853 0 1 Wh853_July_04_2020_28742595 Wh853_July_04_2020_35526592 Wh853 0 2 Wh853_July_05_2020_28491411 Wh853_July_05_2020_35602397 Wh853 0 3 Wh853_July_06_2020_27181307 Wh853_July_06_2020_34321668 Wh853 0 4 Wh853_July_07_2020_28299965 Wh853_July_07_2020_35496802 Wh853 0 5 Wh853_July_08_2020_28442846 Wh853_July_08_2020_35378955 Note: Wh840, Wh845, Wh848, Wh853, Wh422, Wh423, and Wh470 had more than 3 days of song counts collected. These birds' scores were averaged across three sessions similar to other birds. They were used for correlating protein levels with motif counts. --------------------------------------------- ## Materials & Methods The audio files can be played in any of these three programs and likely others. - Windows Media Player: One can listen to audio - Audacity: https://www.audacityteam.org/. One can listen to audio and view it as spectrogram. Data were originally viewed in this program for the publication prior to processing via the Vocal Inventory Clustering Engine mentioned in citation above. --------------------------------------------- ## Contributor Roles The roles are defined by the CRediT taxonomy http://credit.niso.org/ - Cesar Medina, University of Arizona: Conceptualization, Data curation, Formal Analysis, Methodology, Software, Investigation, Validation, Visualization, Writing-original draft, Writing-review & editing - Eddie Vargas, University of Arizona: Data curation, Formal Analysis, Writing-review & editing - Stephanie J. Munger, University of Arizona: Data curation, Methodology, Writing-review & editing - Julie E. Miller, University of Arizona: Conceptualization, Data curation, Formal analysis, Project Administration, Resources, Supervision, Validation, Visualization, Writing-original draft, Writing-review & editing --------------------------------------------- ## Additional Notes Contact the Corresponding Author if you would like additional information. Images of syllables types and PowerPoints of predefined motifs available upon request.